environment_osx.txt

# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
aioeasywebdav=2.2.0
apipkg=1.4
appdirs=1.4.3
argcomplete=1.8.2
argh=0.26.2
arrow-cpp=0.8.0
asn1crypto=0.24.0
atomicwrites=1.1.5
atropos=1.1.18
attrs=18.1.0
backcall=0.1.0
backports=1.0
backports.functools_lru_cache=1.5
bcftools=1.7
bcrypt=3.1.3
beautifulsoup4=4.6.0
bedtools=2.27.1
bioconductor-all=1.20.0
bioconductor-annotate=1.56.0
bioconductor-annotationdbi=1.40.0
bioconductor-annotationhub=2.10.1
bioconductor-biobase=2.38.0
bioconductor-biocgenerics=0.24.0
bioconductor-biocinstaller=1.28.0
bioconductor-biocparallel=1.12.0
bioconductor-biocviews=1.46.0
bioconductor-biomart=2.34.2
bioconductor-biostrings=2.46.0
bioconductor-clusterprofiler=3.6.0
bioconductor-complexheatmap=1.17.1
bioconductor-consensusclusterplus=1.42.0
bioconductor-degreport=1.14.0
bioconductor-delayedarray=0.4.1
bioconductor-deseq2=1.18.1
bioconductor-do.db=2.9
bioconductor-dose=3.4.0
bioconductor-dupradar=1.8.0
bioconductor-edger=3.20.7
bioconductor-fgsea=1.2.1
bioconductor-genefilter=1.60.0
bioconductor-geneplotter=1.56.0
bioconductor-genomeinfodb=1.14.0
bioconductor-genomeinfodbdata=1.0.0
bioconductor-genomicalignments=1.14.1
bioconductor-genomicfeatures=1.30.3
bioconductor-genomicranges=1.30.3
bioconductor-go.db=3.5.0
bioconductor-gosemsim=2.2.0
bioconductor-graph=1.56.0
bioconductor-hsmmsinglecell=0.112.0
bioconductor-interactivedisplaybase=1.16.0
bioconductor-iranges=2.12.0
bioconductor-limma=3.34.9
bioconductor-monocle=2.6.0
bioconductor-qvalue=2.10.0
bioconductor-rbgl=1.54.0
bioconductor-rsamtools=1.30.0
bioconductor-rsubread=1.28.1
bioconductor-rtracklayer=1.38.3
bioconductor-s4vectors=0.16.0
bioconductor-summarizedexperiment=1.8.0
bioconductor-sva=3.26.0
bioconductor-tximport=1.6.0
bioconductor-xvector=0.18.0
bioconductor-zlibbioc=1.24.0
biopython=1.70
blas=1.1
bleach=1.4.2
blinker=1.4
bokeh=0.12.16
boost=1.64.0
boost-cpp=1.64.0
boto3=1.7.28
botocore=1.10.28
bowtie=1.2.2
bowtie2=2.3.4.1
bzip2=1.0.6
ca-certificates=2018.4.16
cachetools=2.0.1
cairo=1.14.6
certifi=2018.4.16
cffi=1.11.5
chardet=3.0.4
click=6.7
cloog=0.18.0
cloudpickle=0.5.3
colormath=3.0.0
configargparse=0.12.0
cryptography=2.2.1
curl=7.54.1
cutadapt=1.16
cycler=0.10.0
cython=0.28.3
cytoolz=0.9.0.1
dask=0.17.5
dask-core=0.17.5
datrie=0.7.1
dbus=1.11.0
decorator=4.3.0
deeptools=3.0.2
distributed=1.21.8
docutils=0.14
dropbox=7.3.1
entrypoints=0.2.3
execnet=1.5.0
expat=2.2.5
fastq-screen=0.11.3
fastqc=0.11.7
feedgenerator=1.9
filechunkio=1.6
font-ttf-dejavu-sans-mono=2.37
fontconfig=2.12.1
freetype=2.7
ftputil=3.2
future=0.16.0
gat=1.3.5
gcc=4.8.5
gettext=0.19.8.1
gffutils=0.9
ghostscript=9.18
ghp-import=0.5.5
giflib=5.1.4
glib=2.51.4
gmp=6.1.2
goatools=0.7.11
google-auth=1.2.1
google-auth-httplib2=0.0.2
google-cloud-core=0.24.1
google-cloud-storage=1.1.1
google-resumable-media=0.0.2
googleapis-common-protos=1.5.3
graphite2=1.3.11
graphviz=2.38.0
greenlet=0.4.13
gsl=2.2.1
h5py=2.7.0
harfbuzz=1.4.3
hdf5=1.8.17
heapdict=1.0.0
hisat2=2.1.0
html5lib=1.0.1
htslib=1.7
httplib2=0.11.1
icu=58.2
idna=2.6
idna_ssl=1.0.0
intervalstats=1.01
ipykernel=4.8.2
ipython=6.4.0
ipython_genutils=0.2.0
ipywidgets=7.2.1
isl=0.12.2
jemalloc=4.5.0
jinja2=2.10
jmespath=0.9.3
joblib=0.11
jpeg=9b
jsonschema=2.6.0
kallisto=0.44.0
krb5=1.14.6
libffi=3.2.1
libgd=2.2.5
libgfortran=3.0.0
libiconv=1.15
libpng=1.6.28
libprotobuf=3.5.2
libsodium=1.0.16
libssh2=1.8.0
libtiff=4.0.7
libtool=2.4.6
libuuid=1.0.3
libwebp=0.5.2
libxcb=1.13
libxml2=2.9.5
locket=0.2.0
lzo=2.10
lzstring=1.0.3
markdown=2.6.11
markupsafe=1.0
matplotlib=2.1.1
mccabe=0.6.1
mistune=0.8.3
mmtf-python=1.1.2
more-itertools=4.1.0
mpc=1.1.0
mpfr=3.1.5
msgpack-python=0.5.6
multidict=4.3.1
multiqc=1.5a
mysql-connector-c=6.1.6
nb_conda=2.2.1
nb_conda_kernels=2.1.0
nbconvert=5.3.1
nbformat=4.4.0
ncurses=5.9
neovim=0.2.6
networkx=2.0
numexpr=2.6.5
numpy=1.12.1
olefile=0.45.1
openblas=0.2.20
openjdk=8.0.121
openssl=1.0.2o
packaging=17.1
pandas=0.23.0
pandoc=2.2.1
pandocfilters=1.4.2
pango=1.40.4
paramiko=2.4.1
parquet-cpp=1.4.0.pre
parso=0.2.1
partd=0.3.8
patsy=0.5.0
pcre=8.39
pelican=3.7.1
perl=5.22.0.1
perl-gd=2.56
perl-gdgraph=1.49
perl-gdtextutil=0.86
pexpect=4.5.0
picard=2.18.5
pickleshare=0.7.4
pigz=2.3.4
pillow=4.3.0
pip=9.0.3
pixman=0.34.0
plotly=2.7.0
pluggy=0.6.0
preseq=2.0.3
prettytable=0.7.2
prompt_toolkit=1.0.15
protobuf=3.5.2
psutil=5.4.5
ptyprocess=0.5.2
py=1.5.3
py2bit=0.3.0
pyarrow=0.8.0
pyasn1=0.4.2
pyasn1-modules=0.0.5
pybedtools=0.7.10
pybigwig=0.3.6
pycodestyle=2.3.1
pycparser=2.18
pydot=1.2.4
pyfaidx=0.5.3
pygments=2.2.0
pygraphviz=1.3.1
pynacl=1.1.2
pyparsing=2.2.0
pyqt=5.6.0
pysam=0.14.1
pysftp=0.2.9
pytables=3.3.0
pytest=3.6.0
pytest-forked=0.2
pytest-runner=4.2
pytest-xdist=1.22.2
python=3.6.3
python-dateutil=2.7.3
python-irodsclient=0.7.0
python-wget=3.2
pytz=2018.4
pyyaml=3.12
pyzmq=17.0.0
qt=5.6.2
qtconsole=4.3.1
r-abind=1.4_5
r-acepack=1.4.1
r-ape=5.1
r-assertthat=0.2.0
r-backports=1.1.2
r-base=3.4.1
r-base64enc=0.1_3
r-bh=1.66.0_1
r-bindr=0.1.1
r-bindrcpp=0.2
r-bit=1.1_12
r-bit64=0.9_5
r-bitops=1.0_6
r-blob=1.1.1
r-broom=0.4.4
r-caret=6.0_79
r-catools=1.17.1
r-checkmate=1.8.5
r-circlize=0.4.3
r-class=7.3_14
r-cli=1.0.0
r-cluster=2.0.6
r-codetools=0.2_15
r-colorspace=1.3_2
r-combinat=0.0_8
r-cowplot=0.9.2
r-crayon=1.3.4
r-crosstalk=1.0.0
r-curl=3.2
r-cvst=0.2_1
r-data.table=1.10.4
r-dbi=1.0.0
r-ddalpha=1.3.3
r-ddrtree=0.1.5
r-densityclust=0.3
r-deoptimr=1.0_8
r-devtools=1.13.5
r-dichromat=2.0_0
r-diffusionmap=1.1_0
r-digest=0.6.15
r-dimred=0.1.0
r-diptest=0.75_7
r-doparallel=1.0.11
r-dosnow=1.0.16
r-dplyr=0.7.4
r-drr=0.0.3
r-dt=0.4
r-dtw=1.18_1
r-evaluate=0.10.1
r-fastica=1.2_0
r-fastmatch=1.1_0
r-fitdistrplus=1.0_9
r-flexmix=2.3_14
r-fnn=1.1
r-foreach=1.4.4
r-foreign=0.8_67
r-formatr=1.5
r-formula=1.2_1
r-fpc=2.1_10
r-futile.logger=1.4.3
r-futile.options=1.0.0
r-gdata=2.18.0
r-geometry=0.3_6
r-getopt=1.20.0
r-getoptlong=0.1.6
r-ggplot2=2.2.1
r-ggrepel=0.8.0
r-ggridges=0.5.0
r-git2r=0.19.0
r-globaloptions=0.0.12
r-glue=1.2.0
r-gower=0.1.2
r-gplots=3.0.1
r-gridbase=0.4_7
r-gridextra=2.3
r-gtable=0.2.0
r-gtools=3.5.0
r-hexbin=1.27.2
r-highr=0.6
r-hmisc=4.0_3
r-hms=0.3
r-htmltable=1.9
r-htmltools=0.3.6
r-htmlwidgets=1.0
r-httpuv=1.3.6.2
r-httr=1.3.1
r-ica=1.0_1
r-igraph=1.2.1
r-ipred=0.9_6
r-irlba=2.3.2
r-iterators=1.0.9
r-jsonlite=1.5
r-kernlab=0.9_25
r-kernsmooth=2.23_15
r-knitr=1.20
r-knitrbootstrap=1.0.1
r-labeling=0.3
r-lambda.r=1.2
r-lars=1.2
r-lattice=0.20_34
r-latticeextra=0.6_28
r-lava=1.6.1
r-lazyeval=0.2.1
r-lmtest=0.9_35
r-locfit=1.5_9.1
r-logging=0.7_103
r-lubridate=1.7.4
r-magic=1.5_6
r-magrittr=1.5
r-markdown=0.8
r-mass=7.3_48
r-matrix=1.2_14
r-matrixmodels=0.4_1
r-matrixstats=0.53.1
r-mclust=5.4
r-memoise=1.1.0
r-metap=0.8
r-mgcv=1.8_17
r-mime=0.5
r-mixtools=1.1.0
r-mnormt=1.5_5
r-modelmetrics=1.1.0
r-modeltools=0.2_21
r-munsell=0.4.3
r-mvtnorm=1.0_6
r-nlme=3.1_131
r-nmf=0.21.0
r-nnet=7.3_12
r-nozzle.r1=1.1_1
r-numderiv=2016.8_1
r-openssl=1.0.1
r-pbapply=1.3_3
r-pheatmap=1.0.8
r-pillar=1.2.2
r-pkgconfig=2.0.1
r-pkgmaker=0.22
r-plogr=0.1_1
r-plotly=4.7.1
r-plyr=1.8.4
r-png=0.1_7
r-prabclus=2.2_6
r-prettyunits=1.0.2
r-prodlim=2018.04.18
r-progress=1.1.2
r-proxy=0.4_17
r-psych=1.5.8
r-purrr=0.2.4
r-qlcmatrix=0.9.5
r-quantreg=5.33
r-r.methodss3=1.7.1
r-r.oo=1.21.0
r-r.utils=2.6.0
r-r6=2.2.2
r-ranger=0.7.0
r-rann=2.5.1
r-rcolorbrewer=1.1_2
r-rcpp=0.12.15
r-rcpparmadillo=0.7.800.2.0
r-rcppeigen=0.3.3.4.0
r-rcppprogress=0.4
r-rcpproll=0.2.2
r-rcurl=1.95_4.8
r-readr=1.1.1
r-recipes=0.1.2
r-registry=0.5
r-reshape=0.8.7
r-reshape2=1.4.3
r-reticulate=1.7
r-rjson=0.2.15
r-rlang=0.2.0
r-rmarkdown=1.9
r-rmysql=0.10.13
r-rngtools=1.2.4
r-robustbase=0.92_7
r-rocr=1.0_7
r-rpart=4.1_13
r-rprojroot=1.3_2
r-rsqlite=2.0
r-rstudioapi=0.7
r-rtsne=0.13
r-runit=0.4.31
r-rvcheck=0.0.9
r-scales=0.5.0
r-scatterplot3d=0.3_40
r-sdmtools=1.1_221
r-segmented=0.5_2.1
r-seurat=2.3.1
r-sfsmisc=1.1_1
r-shape=1.4.3
r-shiny=1.0.5
r-slam=0.1_40
r-sn=1.5_0
r-snow=0.4_2
r-sourcetools=0.1.6
r-sparsem=1.76
r-squarem=2017.10_1
r-stringi=1.1.7
r-stringr=1.2.0
r-survival=2.40_1
r-tclust=1.3_1
r-tibble=1.4.2
r-tidyr=0.8.1
r-tidyselect=0.2.4
r-timedate=3012.100
r-trimcluster=0.1_2
r-tsne=0.1_3
r-upsetr=1.3.3
r-utf8=1.1.3
r-vgam=1.0_3
r-viridis=0.5.1
r-viridislite=0.3.0
r-whisker=0.3_2
r-withr=2.1.1
r-xml=3.98_1.6
r-xtable=1.8_2
r-yaml=2.1.18
r-zoo=1.8_1
ratelimiter=1.2.0
readline=6.2
reportlab=3.4.0
requests=2.13.0
rpy2=2.8.5
rsa=3.1.4
s3transfer=0.1.13
salmon=0.10.0
samtools=1.7
scikit-learn=0.19.1
scipy=1.1.0
seaborn=0.8.1
send2trash=1.5.0
setuptools=39.2.0
simplegeneric=0.8.1
simplejson=3.8.1
singledispatch=3.4.0.3
sip=4.18
six=1.11.0
snakemake=4.4.0
sortedcontainers=2.0.2
spectra=0.0.11
sqlite=3.13.0
sra-tools=2.8.2
statsmodels=0.9.0
subread=1.6.1
tbb=2018_20171205
tblib=1.3.2
terminado=0.8.1
testpath=0.3.1
tk=8.5.19
toolz=0.9.0
tornado=5.0.2
tqdm=4.7.2
trackhub=0.2.4
traitlets=4.3.2
ucsc-bedsort=357
ucsc-bedtobigbed=357
ucsc-fetchchromsizes=357
ucsc-gtftogenepred=357
ucsc-liftover=357
ucsc-oligomatch=357
ucsc-twobittofa=357
unidecode=1.0.22
urllib3=1.12
watermark=1.6.0
wcwidth=0.1.7
webencodings=0.5
wget=1.18
wgetter=0.7
wheel=0.31.0
widgetsnbextension=3.2.1
wrapt=1.10.11
xlrd=1.1.0
xlsxwriter=1.0.4
xmlrunner=1.7.7
xopen=0.3.2
xorg-kbproto=1.0.7
xorg-libice=1.0.9
xorg-libsm=1.2.2
xorg-libx11=1.6.5
xorg-libxau=1.0.8
xorg-libxdmcp=1.1.2
xorg-libxext=1.3.3
xorg-libxrender=0.9.10
xorg-renderproto=0.11.1
xorg-xextproto=7.3.0
xorg-xproto=7.0.31
xz=5.2.3
yaml=0.1.7
yarl=1.2.3
zeromq=4.2.5
zict=0.1.3
zlib=1.2.11